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Without knowing any better at the time, I too planted java fern in the substrate but it is doing just fine. Mine however was green and healthy when I bought it. Almost immediately black spots appeared on the underside of the leaves. I didn't know what was happening until roots began to appear and grow downward. Then teeny tiny leaves started to appear and I learned that this was sporangia (spores cases) from which "daughter plants develop. Now I am trying to learn what happens next.
 
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